He said the government had interfered in his efforts to pursue those responsible for corruption at the privately-owned Kabul Bank.
Mr Fitrat was speaking from the US where he has residency. He says he will not return to Afghanistan.
An Afghan government spokesman said the resignation amounted to treason.
Waheed Omar, Afghan President Hamid Karzai's spokesman, also added that Mr Fitrat was himself under investigation.
"My life was completely in danger and this was particularly true after I spoke to the parliament and exposed some people who are responsible for the crisis of Kabul Bank," Mr Fitrat said on Monday.
The embezzlement at Kabul Bank, Afghanistan's largest private bank, almost led to its collapse last year after it was discovered that hundreds of millions of dollars had gone missing. The bank handles up to 80% of the government payroll, including salaries for policemen and teachers.
A run on the bank was only avoided by the injection of massive amounts of public funds and government guarantees.
'Investigation blocked'Investigators say that the bank made hundreds of millions of dollars of inappropriate loans. It was founded in 2004 by Sherkhan Farnood, a leading international poker player.
The bank was bailed out in September, which is when the central bank also took control of its finances. Mr Fitrat, as president of the central bank, was in charge of an investigation into what went wrong.
Continue reading the main story 2004: Kabul Bank founded by international poker player, Sherkhan FarnoodSeptember 2010: Kabul Bank taken over by the central bank after a run on the bank amid fears of its collapseFebruary 2011: Abdul Qadeer Fitrat, central bank governor, tells BBC those involved in bank's woes should be prosecutedFebruary 2011: An IMF report recommends the bank be put in receivershipApril 2011: Mr Fitrat, names in parliament prominent Afghan figures in connection with the Kabul Bank scandalMay 2011: Report by anti-corruption office shows $467m (?290m) of outstanding loans were made without appropriate collateralAs the crisis at Kabul Bank unfolded, President Karzai pledged to fully investigate those involved in the crisis.But Mr Fitrat alleges that the central government did not assist him in the investigation or provide any help in recovering the bank's assets.
"During [the] last 10 months during Kabul Bank crisis, I continuously pressed for the creation of a special prosecution, for the creation of a special tribunal to investigate and prosecute those who were involved in Kabul Bank's fraud," he told the BBC.
"I did not receive any information that there is a credible plan to prosecute, to investigate and prosecute these individuals. The high political authorities of the country was responsible [for blocking] these efforts," he alleged.
He said he left the country after he received information that his life was in danger from "credible sources".
In April, Mr Fitrat publicly named in parliament high-profile figures who were allegedly involved in the near collapse of the bank.
Relatives of President Karzai, including his brother, Mahmoud Karzai, were among those named in connection with the scandal. Mr Fitrat also implicated the brother of Vice-President Qasim Fahim.
Both men - who were major shareholders in the bank - deny the charges. They say they are being targeted because of their position
'Foreign advisers' Kabul Bank was taken over by the Afghan central bank in September 2010President Karzai has said Afghanistan lacks the necessary banking experience to oversee the institution and has blamed foreign advisers for the crisis.
He has also pledged to ensure that those responsible are subject to criminal investigations.
The International Monetary Fund wants the Afghan government to wind down Kabul Bank before it releases the funds for a new assistance programme. A recent IMF report said the bank should be placed in receivership.
Britain has already suspended a $140m (?85.6m) payment in aid to the country following the crisis.
"We take note of Governor Fitrat's decision to step down as central bank governor," IMF spokesman Raphael Anspach is quoted by the Wall Street Journal as saying.
"We look forward to continue discussing with his successor ways to improve the Afghan banking system in the period ahead."
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